knox / AlphaFold-readme-10.sh
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| 1 | $DOWNLOAD_DIR/ # Total: ~ 2.62 TB (download: 556 GB) |
| 2 | bfd/ # ~ 1.8 TB (download: 271.6 GB) |
| 3 | # 6 files. |
| 4 | mgnify/ # ~ 120 GB (download: 67 GB) |
| 5 | mgy_clusters_2022_05.fa |
| 6 | params/ # ~ 5.3 GB (download: 5.3 GB) |
| 7 | # 5 CASP14 models, |
| 8 | # 5 pTM models, |
| 9 | # 5 AlphaFold-Multimer models, |
| 10 | # LICENSE, |
knox / AlphaFold-readme-9.sh
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| 1 | scripts/download_all_data.sh <DOWNLOAD_DIR> reduced_dbs |
knox / AlphaFold-readme-8.sh
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| 1 | scripts/download_all_data.sh <DOWNLOAD_DIR> |
knox / AlphaFold-readme-7.sh
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| 1 | python3 docker/run_docker.py \ |
| 2 | --fasta_paths=your_protein.fasta \ |
| 3 | --max_template_date=2022-01-01 \ |
| 4 | --data_dir=$DOWNLOAD_DIR \ |
| 5 | --output_dir=/home/user/absolute_path_to_the_output_dir |
knox / AlphaFold-readme-6.sh
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| 1 | pip3 install -r docker/requirements.txt |
knox / AlphaFold-readme-5.sh
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| 1 | W: GPG error: https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64 InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY A4B469963BF863CC |
| 2 | E: The repository 'https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64 InRelease' is not signed. |
knox / AlphaFold-readme-4.sh
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| 1 | docker build -f docker/Dockerfile -t alphafold . |
knox / AlphaFold-readme-3.sh
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| 1 | docker run --rm --gpus all nvidia/cuda:11.0-base nvidia-smi |
knox / AlphaFold-readme-2.sh
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| 1 | scripts/download_all_data.sh <DOWNLOAD_DIR> > download.log 2> download_all.log & |
knox / AlphaFold-readme-1.sh
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| 1 | git clone https://github.com/deepmind/alphafold.git |
| 2 | cd ./alphafold |